LAMMPS (4 May 2017)
  using 1 OpenMP thread(s) per MPI task

units           metal

atom_style      atomic
atom_modify     map array
boundary        p p p
atom_modify	sort 0 0.0

# temperature

variable t equal 1800.0

# coordination number cutoff

variable r equal 2.835

# minimization parameters

variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1

# diamond unit cell

variable a equal 5.431
lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431

region          myreg block     0 4                                 0 4                                 0 4
create_box      1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
  1 by 1 by 1 MPI processor grid
create_atoms    1 region myreg
Created 512 atoms

mass            1       28.06

group Si type 1
512 atoms in group Si

velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian

# make a vacancy

group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511

pair_style      edip
pair_coeff * * Si.edip Si
Reading potential file Si.edip with DATE: 2011-09-15

thermo          10

fix             1 all nvt temp $t $t 0.1
fix             1 all nvt temp 1800 $t 0.1
fix             1 all nvt temp 1800 1800 0.1

timestep        1.0e-3
neighbor        1.0 bin
neigh_modify    every 1 delay 10 check yes

# equilibrate

run             500
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.12138
  ghost atom cutoff = 4.12138
  binsize = 2.06069, bins = 11 11 11
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair edip, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1802.5039   -2372.6618            0   -2253.8359    12261.807 
      10    952.62744    -2316.428            0   -2253.6283    723.08283 
      20      549.138    -2289.442            0   -2253.2413   -2444.5194 
      30    1047.0106   -2321.1522            0   -2252.1305    9013.2015 
      40    663.46143   -2294.2083            0   -2250.4711    2942.5358 
      50    504.74533    -2282.849            0   -2249.5748   -461.44817 
      60    1019.2173   -2315.5639            0   -2248.3744     7706.429 
      70    844.51197   -2302.5251            0   -2246.8526    3116.8313 
      80    814.90406   -2299.3372            0   -2245.6165    794.77536 
      90    1269.5635   -2327.4775            0   -2243.7845    7729.3971 
     100    977.61566   -2306.1118            0   -2241.6647    2969.9952 
     110    843.08538   -2295.6547            0   -2240.0763    1393.4046 
     120    1161.6968   -2314.6587            0   -2238.0766    7398.3495 
     130    918.19453   -2296.4321            0   -2235.9022    2537.4011 
     140    881.42546   -2292.2768            0   -2234.1709    1550.3345 
     150    1231.1005   -2313.1054            0   -2231.9479    8112.7568 
     160    967.01865    -2293.332            0   -2229.5836     3422.964 
     170    833.51246   -2282.7489            0   -2227.8015     43.99251 
     180    1240.8487   -2307.3633            0   -2225.5632    6557.8652 
     190    1126.4621   -2297.1922            0   -2222.9328    4289.0083 
     200     947.5957     -2283.29            0   -2220.8219    586.28203 
     210     1228.153   -2299.4702            0   -2218.5071    5315.0427 
     220    1215.4104   -2295.9407            0   -2215.8176     4870.343 
     230     1112.436   -2286.7552            0   -2213.4204    2527.1887 
     240     1300.081   -2296.6013            0   -2210.8965    5738.3711 
     250    1192.5739   -2286.8463            0   -2208.2286    4076.4913 
     260    1004.7055   -2272.1753            0   -2205.9424     359.3769 
     270    1241.2018   -2285.3632            0   -2203.5399    4160.5764 
     280    1360.1974    -2290.325            0   -2200.6572    5802.3912 
     290    1151.9366   -2273.9467            0    -2198.008    1418.8905 
     300    1174.3518   -2273.0089            0   -2195.5925    1998.2297 
     310    1329.2726   -2280.5049            0   -2192.8757    4721.7304 
     320    1284.4414   -2274.7519            0   -2190.0781    2985.4687 
     330    1328.3761   -2274.9545            0   -2187.3844    4543.2115 
     340    1446.3847   -2279.8693            0   -2184.5198    6254.4071 
     350    1366.2165   -2271.7475            0   -2181.6828    3637.8351 
     360    1358.9609   -2268.5982            0   -2179.0118    3049.5811 
     370    1552.2079   -2278.4802            0   -2176.1545    6334.0061 
     380    1562.5295   -2276.1793            0   -2173.1731    5787.5565 
     390    1415.5498   -2263.7823            0   -2170.4655    3438.5782 
     400    1323.1568   -2255.1641            0    -2167.938    2427.2311 
     410    1260.7186   -2248.5373            0   -2165.4273    1208.6316 
     420    1282.1118   -2247.3718            0   -2162.8516    462.65508 
     430    1451.9439   -2255.7551            0   -2160.0391    2037.8027 
     440    1568.9415    -2260.417            0   -2156.9882    3531.1613 
     450    1565.8261   -2257.2396            0   -2154.0161    2586.7896 
     460    1677.7143   -2261.7214            0    -2151.122     4112.976 
     470    1762.9071   -2264.4244            0   -2148.2089    5053.2148 
     480    1704.5898   -2257.8678            0   -2145.4966    4077.4649 
     490    1731.2619   -2257.1048            0   -2142.9753    4710.5276 
     500    1723.9777    -2254.161            0   -2140.5118    4760.7316 
Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms

Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.28525    | 0.28525    | 0.28525    |   0.0 | 91.29
Neigh   | 0.013753   | 0.013753   | 0.013753   |   0.0 |  4.40
Comm    | 0.0033333  | 0.0033333  | 0.0033333  |   0.0 |  1.07
Output  | 0.00071096 | 0.00071096 | 0.00071096 |   0.0 |  0.23
Modify  | 0.008044   | 0.008044   | 0.008044   |   0.0 |  2.57
Other   |            | 0.001385   |            |       |  0.44

Nlocal:    511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    845 ave 845 max 845 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  7902 ave 7902 max 7902 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7902
Ave neighs/atom = 15.4638
Neighbor list builds = 19
Dangerous builds = 0

Total wall time: 0:00:00
